Does the 9% corporate tax still apply if I hold property through a free zone company?

Yes, a free zone won't shield it. Income from UAE immovable property is always treated as non-qualifying income for a Qualifying Free Zone Person, so a free zone company's rent or gain from a mainland Dubai property is taxed at the standard 9%, regardless of its 0% QFZP status on other activities. Get any structuring reviewed before relying on a free zone entity.